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AvilPage / kraken-db-builder

Build standard & custom kraken2 database indexes with single command
https://avilpage.com/kdb.html
MIT License
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Returned non-zero exit status 254 #1

Open jarrodscott opened 1 week ago

jarrodscott commented 1 week ago

Thanks for sharing this amazing tool! I am running like this:

kdb --db-type standard --threads 30 --cache-dir .

And I continue to get an error like this:

subprocess.CalledProcessError: Command 'ncbi-genome-download --section refseq \
--format fasta --assembly-level complete --retries 3 --parallel 30 --progress-bar plasmid' \
returned non-zero exit status 254.

In line 23 of kdb.py I tried moving plasmid to the end of the list, sohuman is next. But I get the same error. Any thoughts. And is the a better place to post this question? Thanks!!

ChillarAnand commented 1 week ago

@jarrodscott Thanks for creating the issue. I will take a look and let you know shortly.

leonmhartman commented 3 days ago

Plasmid fails because it isn't one of the "SUPPORTED_TAXONOMIC_GROUPS" listed in the config.py file of the ncbi-genome-download tool, which kdb uses to retrieve data from NCBI. Neither are "human" or "UniVec_Core", so these will fail too if you're running kdb to create a "standard" kraken2 database.